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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 0include - 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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 0
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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0include - 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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0
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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0include - 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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0
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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0include - 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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0
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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0include - 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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0
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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ), 'gf_id' => 'HOM05D001188', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001188' ), 'data_identifier' => 'HOM05D001188', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001188', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '525', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03390' => 'bna', 'A02p15090' => 'bna', 'A03p07560' => 'bna', 'A03p33020' => 'bna', 'A05p45270' => 'bna', 'A06p08380' => 'bna', 'A07p32000' => 'bna', 'A07p34890' => 'bna', 'A08p32320' => 'bna', 'A09p62990' => 'bna', 'A10p22930' => 'bna', 'Aa31LG11G13500' => 'aar', 'Aa31LG1G1540' => 'aar', 'Actinidia14893' => 'ach', 'Actinidia16655' => 'ach', 'Actinidia18933' => 'ach', 'Actinidia35089' => 'ach', 'Actinidia36318' => 'ach', 'Ah.03g137620' => 'amhyb', 'Ah.10g037760' => 'amhyb', 'Ah.16g101780' => 'amhyb', 'AL1G25130' => 'aly', 'AL2G27350' => 'aly', 'AL3G11920' => 'aly', 'AL6G26990' => 'aly', 'Aqoxy3G00294' => 'aox', 'Aqoxy3G03954' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03CGRD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0MP6BV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.34XY90' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4VI3XS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.61ZXLU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DW64SD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JCH4FE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K09X2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LU8TWQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RT9W1M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YP19K2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z3Y2S3' => 'arhy', 'AT1G13390' => 'ath', 'AT1G68490' => 'ath', 'AT3G02555' => 'ath', 'AT5G16110' => 'ath', 'ATR0582G282' => 'atr', 'ATR1125G036' => 'atr', 'Atru.chr1.1702' => 'acertr', 'Atru.chr11.96' => 'acertr', 'Atru.chr9.860' => 'acertr', 'AUR62002861' => 'cqu', 'AUR62008997' => 'cqu', 'AUR62023304' => 'cqu', 'AUR62035213' => 'cqu', 'BcaB01g05003' => 'bca', 'BcaB01g05005' => 'bca', 'BcaB03g13143' => 'bca', 'BcaB03g15421' => 'bca', 'BcaB03g15825' => 'bca', 'BcaB05g24388' => 'bca', 'BcaB08g34292' => 'bca', 'BcaC01g04438' => 'bca', 'BcaC01g04559' => 'bca', 'BcaC03g14958' => 'bca', 'BcaC03g18468' => 'bca', 'BcaC05g25049' => 'bca', 'BcaC05g30368' => 'bca', 'BcaC07g38690' => 'bca', 'BcaC07g41643' => 'bca', 'BcaC08g45969' => 'bca', 'BcaC08g46274' => 'bca', 'BcaC09g47709' => 'bca', 'BcaNung02222' => 'bca', 'BcaNung05406' => 'bca', 'BNapus_Darmor_BZH_scaffold_122p00050' => 'bna', 'BNapus_Darmor_BZH_scaffold_99p00070' => 'bna', 'BolC1t05896H' => 'bol', 'BolC2t06738H' => 'bol', 'BolC2t08568H' => 'bol', 'BolC3t13375H' => 'bol', 'BolC3t14340H' => 'bol', 'BolC5t29730H' => 'bol', 'BolC5t35074H' => 'bol', 'BolC6t38862H' => 'bol', 'BolC6t39277H' => 'bol', 'BolC8t49236H' => 'bol', 'BolC8t52197H' => 'bol', 'BolC9t58931H' => 'bol', 'BolSC74t61257H' => 'bol', 'BraA02t05310Z' => 'bra', 'BraA02t06575Z' => 'bra', 'BraA03t10084Z' => 'bra', 'BraA05t23133Z' => 'bra', 'BraA06t24034Z' => 'bra', 'BraA07t30830Z' => 'bra', 'BraA08t35156Z' => 'bra', 'BraA09t41657Z' => 'bra', 'BraA10t44361Z' => 'bra', 'BraSC246t45835Z' => 'bra', 'C02p08150' => 'bna', 'C02p24760' => 'bna', 'C03p08790' => 'bna', 'C03p19600' => 'bna', 'C03p40170' => 'bna', 'C05p09910' => 'bna', 'C06p37590' => 'bna', 'C06p41460' => 'bna', 'C08p16150' => 'bna', 'C08p46450' => 'bna', 'C09p60880' => 'bna', 'C09p75790' => 'bna', 'CAN.G610.80' => 'can', 'CANSAT01G2779' => 'cansat', 'CANSAT78G1507' => 'cansat', 'CANSAT80G0425' => 'cansat', 'CANSAT80G0467' => 'cansat', 'CARHR013760' => 'chi', 'CARHR061270' => 'chi', 'CARHR076560' => 'chi', 'CARHR197190' => 'chi', 'Carub.0001s1310' => 'cru', 'Carub.0002s1500' => 'cru', 'Carub.0003s0167' => 'cru', 'Carub.0006s1430' => 'cru', 'Carub.0055s0003' => 'cru', 'Ca_11171_v3' => 'car', 'Ca_13733_v3' => 'car', 'Ca_25447_v3' => 'car', 'Ca_25492_v3' => 'car', 'CBR_g12347' => 'cbr', 'Cc04_g07110' => 'ccan', 'Cc11_g10110' => 'ccan', 'CDE05G2322' => 'cde', 'CDE06G1178' => 'cde', 'CDE06G1674' => 'cde', 'CDE07G1812' => 'cde', 'Cfa007924' => 'cfa', 'Cfa018592' => 'cfa', 'Cfa019771' => 'cfa', 'Ciclev10012908m.g' => 'ccl', 'Ciclev10016881m.g' => 'ccl', 'Ciclev10022616m.g' => 'ccl', 'CiPaw.03G061300' => 'cil', 'CiPaw.04G042000' => 'cil', 'CiPaw.15G085700' => 'cil', 'CiPaw.15G130700' => 'cil', 'ClCG03G009560' => 'cla', 'ClCG05G011830' => 'cla', 'ClCG05G022670' => 'cla', 'ClCG06G014810' => 'cla', 'COL.COLO4_09325' => 'col', 'COL.COLO4_11306' => 'col', 'COL.COLO4_24805' => 'col', 'Cpa.g.sc1.35' => 'cpa', 'Cpa.g.sc282.12' => 'cpa', 'Cpa.g.sc3.511' => 'cpa', 'CsaV3_1G003820' => 'csa', 'CsaV3_3G020680' => 'csa', 'CsaV3_5G023120' => 'csa', 'CsaV3_5G034370' => 'csa', 'CSS0008362' => 'camsi', 'CSS0009416' => 'camsi', 'CSS0009430' => 'camsi', 'CSS0010207' => 'camsi', 'CSS0033520' => 'camsi', 'DCAR_007246' => 'dca', 'DCAR_011355' => 'dca', 'DCAR_015142' => 'dca', 'DCAR_023657' => 'dca', 'DCAR_026733' => 'dca', 'DCAR_030157' => 'dca', 'Dinv15674' => 'din', 'Dinv21083' => 'din', 'Dinv28104' => 'din', 'Dinv31636' => 'din', 'Dinv33943' => 'din', 'Dinv34823' => 'din', 'Duzib068G0153' => 'dzi', 'Duzib084G1405' => 'dzi', 'Duzib133G1375' => 'dzi', 'Duzib138G1765' => 'dzi', 'Duzib205G0288' => 'dzi', 'Duzib248G1403' => 'dzi', 'Duzib251G0580' => 'dzi', 'Duzib268G1413' => 'dzi', 'ECA233G5311' => 'eca', 'ECA234G4257' => 'eca', 'ECA240G2122' => 'eca', 'ECA246G3804' => 'eca', 'EL10Ac2g04580' => 'bvu', 'EL10Ac6g14395' => 'bvu', 'Eucgr.F02493' => 'egr', 'Eucgr.G02318' => 'egr', 'Eucgr.K02224' => 'egr', 'FAN02G0864' => 'fan', 'FAN04G0161' => 'fan', 'FAN05G2204' => 'fan', 'FAN07G0717' => 'fan', 'FAN07G2096' => 'fan', 'FAN08G0058' => 'fan', 'FAN12G1876' => 'fan', 'FAN12G1991' => 'fan', 'FAN12G3206' => 'fan', 'FAN12G3314' => 'fan', 'FAN13G2404' => 'fan', 'FAN18G0048' => 'fan', 'FAN18G3829' => 'fan', 'FAN22G1332' => 'fan', 'FvH4_4g27320' => 'fve', 'FvH4_4g27321' => 'fve', 'FvH4_5g12120' => 'fve', 'FvH4_6g39201' => 'fve', 'Glyma.05G234000' => 'gma', 'Glyma.07G091800' => 'gma', 'Glyma.08G041300' => 'gma', 'Glyma.08G365500' => 'gma', 'Glyma.10G274000' => 'gma', 'Glyma.13G046100' => 'gma', 'Glyma.18G296700' => 'gma', 'Glyma.19G047100' => 'gma', 'Glyma.20G116000' => 'gma', 'Gohir.A03G147000' => 'ghi', 'Gohir.A04G098400' => 'ghi', 'Gohir.A06G049532' => 'ghi', 'Gohir.A07G173283' => 'ghi', 'Gohir.A09G177300' => 'ghi', 'Gohir.A11G163400' => 'ghi', 'Gohir.A12G054100' => 'ghi', 'Gohir.D02G170100' => 'ghi', 'Gohir.D04G138000' => 'ghi', 'Gohir.D06G049000' => 'ghi', 'Gohir.D07G181000' => 'ghi', 'Gohir.D09G172800' => 'ghi', 'Gohir.D11G169800' => 'ghi', 'Gohir.D12G052700' => 'ghi', 'Gorai.001G201900' => 'gra', 'Gorai.005G190600' => 'gra', 'Gorai.006G194700' => 'gra', 'Gorai.007G181500' => 'gra', 'Gorai.008G055900' => 'gra', 'Gorai.010G055500' => 'gra', 'Gorai.012G122900' => 'gra', 'GSVIVG01008289001' => 'vvi', 'GSVIVG01011892001' => 'vvi', 'GSVIVG01031028001' => 'vvi', 'HanXRQChr08g0213871' => 'han', 'HanXRQChr08g0226061' => 'han', 'HanXRQChr09g0252661' => 'han', 'HanXRQChr15g0476301' => 'han', 'HanXRQChr17g0552291' => 'han', 'Haze_14150' => 'cav', 'Haze_17488' => 'cav', 'Haze_18677' => 'cav', 'Hma1.2p1_0061F.1_g033860' => 'hma', 'Hma1.2p1_0653F.1_g196290' => 'hma', 'HPP92_003773' => 'vpl', 'HPP92_008199' => 'vpl', 'HPP92_020143' => 'vpl', 'HPP92_021597' => 'vpl', 'HPP92_021857' => 'vpl', 'HPP92_023125' => 'vpl', 'HPP92_027123' => 'vpl', 'Hund02389' => 'sun', 'Hund16155' => 'sun', 'Hund20797' => 'sun', 'Hund25061' => 'sun', 'Hund28564' => 'sun', 'Lalb_Chr02g0145951' => 'lal', 'Lalb_Chr02g0158221' => 'lal', 'Lalb_Chr04g0257451' => 'lal', 'Lalb_Chr05g0222501' => 'lal', 'Lalb_Chr06g0166041' => 'lal', 'Lalb_Chr06g0173561' => 'lal', 'Lalb_Chr06g0174581' => 'lal', 'Lalb_Chr14g0371161' => 'lal', 'Lalb_Chr16g0387871' => 'lal', 'Lalb_Chr17g0335871' => 'lal', 'Lalb_Chr21g0308911' => 'lal', 'Lalb_Chr21g0317821' => 'lal', 'Lalb_Chr22g0353071' => 'lal', 'Lalb_Chr24g0397791' => 'lal', 'Lj1g0016648' => 'lja', 'Lj2g0012151' => 'lja', 'Lj2g0014173' => 'lja', 'Lj2g0018195' => 'lja', 'Lj3C1014T9' => 'lonja', 'Lj4g0018774' => 'lja', 'Lj5g0002751' => 'lja', 'Lj6A758T16' => 'lonja', 'Lj9A426G57' => 'lonja', 'Lsat_1_v5_gn_3_59100' => 'lsa', 'Lsat_1_v5_gn_4_17440' => 'lsa', 'Lsat_1_v5_gn_8_146980' => 'lsa', 'Lsat_1_v5_gn_8_40640' => 'lsa', 'Manes.01G011400' => 'mes', 'Manes.01G110300' => 'mes', 'Manes.02G068500' => 'mes', 'Manes.05G137300' => 'mes', 'Manes.06G067600' => 'mes', 'Manes.14G102800' => 'mes', 'Mapoly0047s0036' => 'mpo', 'MBI10_g16030_MAGBIO' => 'mbi', 'MBI11_g43076_MAGBIO' => 'mbi', 'MBI16_g35167_MAGBIO' => 'mbi', 'MD06G1216300' => 'mdo', 'MD09G1252200' => 'mdo', 'MD13G1041500' => 'mdo', 'MD13G1041600' => 'mdo', 'MD14G1226700' => 'mdo', 'MD16G1042400' => 'mdo', 'MD16G1042500' => 'mdo', 'MD17G1244500' => 'mdo', 'Medtr1g051170' => 'mtr', 'Medtr1g110760' => 'mtr', 'Medtr4g087400' => 'mtr', 'Medtr6g018430' => 'mtr', 'Medtr6g084470' => 'mtr', 'Medtr8g104210' => 'mtr', 'MELO3C003023.2' => 'cme', 'MELO3C012253.2' => 'cme', 'MELO3C017306.2' => 'cme', 'MELO3C023804.2' => 'cme', 'Migut.D01477' => 'egut', 'Migut.E00344' => 'egut', 'MSTRG.13534' => 'ama', 'MSTRG.2232' => 'ama', 'MSTRG.23574' => 'ama', 'MSTRG.4507' => 'ama', 'Nitab4.5_0000057g0270' => 'nta', 'Nitab4.5_0000208g0250' => 'nta', 'Nitab4.5_0000659g0090' => 'nta', 'Nitab4.5_0000791g0120' => 'nta', 'Nitab4.5_0000912g0200' => 'nta', 'Nitab4.5_0000974g0070' => 'nta', 'Nitab4.5_0001194g0070' => 'nta', 'Nitab4.5_0002207g0060' => 'nta', 'Nitab4.5_0002207g0080' => 'nta', 'Nitab4.5_0003373g0040' => 'nta', 'Nitab4.5_0006638g0010' => 'nta', 'Nitab4.5_0007985g0050' => 'nta', 'Nitab4.5_0009701g0010' => 'nta', 'Nitab4.5_0009855g0030' => 'nta', 'Nitab4.5_0010671g0010' => 'nta', 'Nitab4.5_0011688g0010' => 'nta', 'Nitab4.5_0013222g0010' => 'nta', 'Nn4g23850' => 'nnu', 'Nn5g30638' => 'nnu', 'Oeu031913.1' => 'oeu', 'Oeu034242.1' => 'oeu', 'Oeu034836.1' => 'oeu', 'Oeu039289.1' => 'oeu', 'Oeu056570.1' => 'oeu', 'Oeu058032.1' => 'oeu', 'Os05g0102500' => 'osa', 'Os12g0600701' => 'osa', 'Peaxi162Scf00013g00106' => 'pax', 'Peaxi162Scf00104g00810' => 'pax', 'Peaxi162Scf00382g00824' => 'pax', 'Peaxi162Scf00634g00025' => 'pax', 'Peaxi162Scf01346g00003' => 'pax', 'PGR004G0549' => 'pgr', 'PGR042G2073' => 'pgr', 'PGR044G0229' => 'pgr', 'PGR083G2588' => 'pgr', 'PGR119G2082' => 'pgr', 'PGSC0003DMG400014545' => 'stu', 'PGSC0003DMG400023107' => 'stu', 'PGSC0003DMG400028791' => 'stu', 'PGSC0003DMG401005720' => 'stu', 'PGSC0003DMG401007748' => 'stu', 'PGSC0003DMG401019589' => 'stu', 'PGSC0003DMG402005720' => 'stu', 'Phvul.002G316300' => 'pvu', 'Phvul.004G065000' => 'pvu', 'Phvul.004G156900' => 'pvu', 'Phvul.007G027500' => 'pvu', 'Phvul.007G248600' => 'pvu', 'Phvul.008G005800' => 'pvu', 'Potri.004G099800' => 'ptr', 'Potri.008G121000' => 'ptr', 'Potri.010G124400' => 'ptr', 'Potri.012G056500' => 'ptr', 'Potri.015G047100' => 'ptr', 'Potri.017G114700' => 'ptr', 'Pp3c14_18120' => 'ppa', 'Pp3c17_20650' => 'ppa', 'Pp3c1_36180' => 'ppa', 'Pp3c20_7460' => 'ppa', 'Pp3c20_7510' => 'ppa', 'Pp3c2_5690' => 'ppa', 'Prupe.1G311600' => 'ppe', 'Prupe.1G311700' => 'ppe', 'Prupe.1G559100' => 'ppe', 'Prupe.3G157300' => 'ppe', 'Prupe.3G161400' => 'ppe', 'Prupe.5G221400' => 'ppe', 'Psat1g037520' => 'psa', 'Psat1g080520' => 'psa', 'Psat2g002080' => 'psa', 'Psat6g224960' => 'psa', 'Psat7g012040' => 'psa', 'PSO017G0291' => 'pso', 'PSO017G4726' => 'pso', 'PSO478G0398' => 'pso', 'PSO478G2914' => 'pso', 'PSO478G2935' => 'pso', 'QL01p042313' => 'qlo', 'QL02p051463' => 'qlo', 'QL10p025341' => 'qlo', 'RcHm_v2.0_Chr4g0435121' => 'rch', 'RcHm_v2.0_Chr4g0435131' => 'rch', 'RcHm_v2.0_Chr7g0185461' => 'rch', 'Rhsim09G0107800' => 'rsi', 'Rhsim10G0067000' => 'rsi', 'Rhsim12G0085100' => 'rsi', 'Sabra04G0080200' => 'sbr', 'Sabra08G0091700' => 'sbr', 'Sabra10G0094500' => 'sbr', 'Sabra15G0038800' => 'sbr', 'Sabra15G0049600' => 'sbr', 'Sabra15G0069000' => 'sbr', 'Sabra15G0070500' => 'sbr', 'Sabra15G0073800' => 'sbr', 'Sabra15G0074000' => 'sbr', 'Sabra15G0074500' => 'sbr', 'Sabra17G0095000' => 'sbr', 'SalBow1G3611' => 'sbo', 'SalBow3G2349' => 'sbo', 'SalBow5G0114' => 'sbo', 'SalBow8G0834' => 'sbo', 'SalBow8G3759' => 'sbo', 'Sc04g0003510' => 'sci', 'Sc04g0006400' => 'sci', 'Sc10g0001180' => 'sci', 'Sc11g0003450' => 'sci', 'Sed0005897' => 'sed', 'Sed0009614' => 'sed', 'Sed0012892' => 'sed', 'Sed0015201' => 'sed', 'Sed0018256' => 'sed', 'Sed0023279' => 'sed', 'Sed0023353' => 'sed', 'Sed0026905' => 'sed', 'SEGI_00322' => 'sgi', 'SEGI_10257' => 'sgi', 'SEGI_25273' => 'sgi', 'SEGI_37570' => 'sgi', 'SEGI_40728' => 'sgi', 'SGA_v2.0_scaffold14G06868' => 'sas', 'SGA_v2.0_scaffold170G38768' => 'sas', 'SGA_v2.0_scaffold33G13493' => 'sas', 'SGA_v2.0_scaffold36G14537' => 'sas', 'SGA_v2.0_scaffold49G18100' => 'sas', 'SMO145G0018' => 'smo', 'SMO197G0029' => 'smo', 'Solyc03g034230.3' => 'sly', 'Solyc03g119480.4' => 'sly', 'Solyc03g119520.4' => 'sly', 'Solyc04g007220.4' => 'sly', 'Solyc05g009360.4' => 'sly', 'Solyc06g069120.3' => 'sly', 'Solyc11g008100.3' => 'sly', 'Solyc12g036650.2' => 'sly', 'Sopen03g007010' => 'spe', 'Sopen03g038330' => 'spe', 'Sopen03g038350' => 'spe', 'Sopen04g002280' => 'spe', 'Sopen05g005150' => 'spe', 'Sopen06g026400' => 'spe', 'Sopen12g017230' => 'spe', 'Sp1g11880' => 'spa', 'Sp3g01590' => 'spa', 'Sp5g23560' => 'spa', 'Sp6g28030' => 'spa', 'TAR371G0579' => 'tar', 'TAR374G1010' => 'tar', 'TAR622G0754' => 'tar', 'TAR629G0241' => 'tar', 'THA.LOC104800007' => 'tha', 'THA.LOC104808279' => 'tha', 'THA.LOC104820949' => 'tha', 'THA.LOC104821931' => 'tha', 'THA.LOC104824029' => 'tha', 'THA.LOC104825699' => 'tha', 'THA.LOC104827157' => 'tha', 'Thecc.02G230100' => 'tca', 'Thecc.03G035200' => 'tca', 'Thecc.04G134100' => 'tca', 'Thhalv10008925m.g' => 'esa', 'Thhalv10014345m.g' => 'esa', 'Thhalv10019181m.g' => 'esa', 'Thhalv10021646m.g' => 'esa', 'TPR.G18798' => 'tpr', 'TPR.G266' => 'tpr', 'TPR.G32445' => 'tpr', 'TPR.G32492' => 'tpr', 'TPR.G32676' => 'tpr', 'TWI15G1206' => 'twi', 'TWI74G0376' => 'twi', 'TWI75G0547' => 'twi', 'TWI79G0396' => 'twi', 'TWI81G0189' => 'twi', 'unitig_10.g29676' => 'ugi', 'unitig_22.g5573' => 'ugi', 'unitig_22.g6556' => 'ugi', 'unitig_22.g6869' => 'ugi', 'unitig_26.g10257' => 'ugi', 'unitig_27.g24915' => 'ugi', 'unitig_699.g19487' => 'ugi', 'unitig_8.g3440' => 'ugi', 'unitig_8.g3981' => 'ugi', 'vmacro01387' => 'vma', 'vmacro05558' => 'vma', 'vmacro10559' => 'vma', 'vmacro17716' => 'vma', 'vmacro23366' => 'vma', 'VMungo0464G0317' => 'vmu', 'VMungo0464G1955' => 'vmu', 'VMungo0720G1100' => 'vmu', 'VMungo0720G1107' => 'vmu', 'VMungo1383G2605' => 'vmu', 'Zm00001eb101540' => 'zma', 'Zm00001eb126970' => 'zma', 'Zm00001eb135520' => 'zma', 'Zm00001eb267620' => 'zma', 'Zm00001eb334130' => 'zma', 'Zm00001eb356260' => 'zma' ) $gf_id = 'HOM05D001188' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001188' ) $data_identifier = 'HOM05D001188' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 25, 'aar' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 4, 'bca' => (int) 20, 'bol' => (int) 13, 'bra' => (int) 10, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 5, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 3, 'fan' => (int) 14, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 7, 'sun' => (int) 5, 'lal' => (int) 14, 'lja' => (int) 6, 'lonja' => (int) 3, 'lsa' => (int) 4, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 6, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 17, 'nnu' => (int) 2, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 5, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 11, 'sbo' => (int) 5, 'sci' => (int) 4, 'sed' => (int) 8, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 8, 'spe' => (int) 7, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 7, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb356260' $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